NAISS Training Newsletter
No 35, 30 January 2025
– Published 30 January 2025
Welcome to the this weeks edition of the NAISS training newsletter. This week we have added the CodeRefinery workshop and remind on a number of training events previously advertised.
The next interactive support session Zoom-in is scheduled for 13 March 2025
ENCCS asked us to share one of their events.
Overview
NAISS training
- Online training workshop: Basic Singularity Running and building Singularity containers - 13 February, 2025
- Online course: Using ParaView and Trame for Scientific Visualisation on HPC resources, 26 February 2025
- Online course: Introduction to Python, March 4, 2025
- Online course: Array computing in C++ using Eigen, 5 March 2025
- Online training seminar: Introduction seminar for Alvis users, 5 March 2025
- Online workshop: Transferring Files to/from HPC Clusters, 7 March 2025
- Online workshop: Introduction to Bianca: Handling Sensitive Research Data, 19 March 2025
- Online course: Introduction to running R, Matlab, and Julia in HPC, 24-26 March 2025
Online interactive support and discussion forum:
- NAISS Zoom-in - a virtual open-house, 13 March from 14:00 until 15:00
CodeRefinery
- Online workshop: CodeRefinery workshop, March 25-27, and April 1-3, 2025
University events
- Online course: Introduction to Linux and UPPMAX, February 10-12, 2025
- Monthly Workshop Series: Whisper Transcription demonstration, starting February 4
ENCCS training
- Online workshop: Julia for High-Performance Data Analysis (Online), 4 - 7 February
NAISS training
Online training workshop: Basic Singularity Running and building Singularity containers - 13 February, 2025
Collaboration between UPPMAX and HPC2N
The online workshop is an introduction to the basic concepts of containerised software environment solutions within the Singularity framework (Sylabs).
During the workshop you will have the opportunity to follow the interactive guide on
- how to run Singularity containers
- how to build your own
- good (and bad) practices on designing and building Singularity recipes
- build and/or host container remotely and what are the limitations
To fully benefit from the workshop, basic Linux system administration experience is highly desirable i.e. knowledge of package management and common tools for building and managing software: git, pip, conda, wget, curl, …
Please follow the instructions to install Singularity (GitHub) on your computer before the workshop.
When: 13 February, 2025
Where: online via Zoom
Registration: Singularity workshop registration form (Google)
For more information and registration, please visit the singularity workshop page (UPPMAX)
Online course: Using ParaView and Trame for Scientific Visualisation on HPC resources, 26 February 2025
This training course introduces scientific visualization using the ParaView application. Participants will first learn the fundamentals of ParaView, including data loading, basic visualization techniques, and essential features for scientific data exploration. During the training, several example data sets will be examined and visualized. We will also show how ParaView can be run on the NAISS resources using hardware-accelerated graphics.
ParaView is a powerful but complex application. Sometimes, a simplified user interface for the visualization pipeline needs to be provided to make a visualization accessible. Kitware has developed the Python-based Trame framework for creating simplified web-based interfaces for visualization pipelines created in ParaView. An example visualization pipeline will be implemented using the Trame framework.
For more information and access to registration visit the scientific visualisation course page (LUNARC).
Online course: Introduction to Python, March 4, 2025
This 1-day course helps you get started with Python, by working through an online and free book. We make use of HPC clusters to write and run Python code. The pace of this highly interactive course is set by the majority of learners, ensuring that any complete beginner has enough time for exercises. At the end of the day, you should feel comfortable with the basics of Python and feel familiar to a book on Python to help you on your next steps.
When: Tuesday, March 4, 2025, 09:00-16:00
Where: online via Zoom
For more information and registration, please visit the Python introduction course page (UPPMAX).
Online course: Array computing in C++ using Eigen, 5 March 2025
This course introduces students to high-performance array computing in C++ using the Eigen library, a versatile template library for linear algebra, matrices, and vectors. Participants will learn to leverage Eigen's expressive syntax and optimized computations for efficient numerical operations. The course covers fundamental concepts such as matrix operations, vector manipulations, and array broadcasting. Through hands-on exercises, students will discover how to use Eigen's powerful features for basic and advanced array operations, gaining essential skills for numerical programming in C++.
For more information and registration, please visit the array computing course page (LUNARC)
Online training seminar: Introduction seminar for Alvis users, 5 March 2025
Description: This seminar is for new and prospective users of the NAISS cluster for AI/ML, Alvis. You will learn all that you need to know to get started on the system.
Time: January 15 13:15-15:00
Registration: Alvis March event registration form (Chalmers)
Online workshop: Transferring Files to/from HPC Clusters, March 7, 2025
In this 3-hour workshop you learn to transfer files to and from Swedish academic HPC clusters. We will cover graphical as well as terminal tools and you will work highly interactively. At the end of the day, you should be comfortable in transferring files between your local computer and a cluster and cross-clusters, and choosing the right tools for your use cases.
The workshop is intended for beginner users but with some Linux experience, see the course link below. You do not need to be a member of a NAISS project in order to join the workshop. A course project on one of the NAISS clusters will be available to those.
When: Tuesday, March 7 2025, 09:00-12:00
Where: online via Zoom
For more information and registration, please visit the file transfer worksop page (UPPMAX).
Online workshop: Introduction to Bianca: Handling Sensitive Research Data, March 19, 2025
Are you just beginning to work with sensitive data in your research? If yes, welcome to a 1-day introduction to handling sensitive data on the UPPMAX cluster, Bianca. We will tell you about NAISS-SENS, how to login to Bianca, transfer files via wharf, basics of the SLURM workload manager and the module system.
The workshop is intended for beginner users of the Bianca cluster.
You do not need to be a member of a NAISS-SENS project in order to join the workshop. A SUPR course project will be available to all participants. The workshop will consist of both lectures and exercise sessions.
When: Wednesday, March 19, 2025
Where: online via Zoom
For more information and registration please visit the Bianca workshop page (UPPMAX).
Online course: Introduction to running R, Matlab, and Julia in HPC, 24-26 March 2025
Cooperation between HPC2N, LUNARC and UPPMAX
Learn how to run R, Matlab, and Julia at Swedish HPC centres, mainly using Tetralith on NSC as an example. We will show you how to find and load the needed modules, how to write a batch script for R, Matlab, and Julia, submitting jobs from inside Matlab, as well as how to install and use your own packages, and more. The course will consist of lectures interspersed with hands-on sessions where you get to try out what you have just learned.
This course will consist of three days. Each day starts at 9:00 and closes 16:00. One day for each language.
Participation is free and open to all current and prospective users of NAISS.
Time and date: 09:00 - 16:00, 24-26 March 2025
Location: online via Zoom
For more information and registration, see:
Online interactive support and discussion forum
Change of date: NAISS Zoom-in - a virtual open-house, 13 March from 14:00 until 15:00
You are invited to a virtual meeting room. Inside the meeting room we like to discuss services offered by NAISS and how they can be used for your computational needs, help you process your data and visualise your results. Participants are highly encouraged to pose their own questions.
We also expect to have experts available from C3SE, HPC2N and LUNARC, to discuss the University operated HPC services at Chalmers, Umeå and Lund University.
The zoom-link for the session will be announced closer to the event.
The following NAISS Zoom-in is planned for 10 April 2025
CodeRefinery events
Online workshop: CodeRefinery workshop, March 25-27, and April 1-3, 2025
Organised by CodeRefinery and partners, including NAISS
Are you writing code and managing data for your research?
Do you feel like wasting too much time on manual work?
Do you struggle to understand and reuse older code?
Join the CodeRefinery workshop 25-27 March and 1-3 April 2025, for free and online.
The workshop covers good coding practices, reproducible research principles, and using Git for collaboration. It consists of streamed lectures and exercises. You may register individually or as a team. In-person exercise sessions are available in some locations.
For registration and more information, please visit the CodeRefinery workshop page (GitHub).
University events
Online course: Introduction to Linux and UPPMAX, February 10-12, 2025
This 3-day course provides an introduction to the high-performance computing (HPC) environment offered at UPPMAX.
It offers an overview on how the systems work and covers skills from basic Linux usage to more advanced tips and tricks. The lectures covering Linux and bash scripting are cluster-agnostic and may be attended by non-UPPMAX users as well.
When: February 10-12, 2025
Where: online via Zoom
For more information and registration, please visit the Linux and UPPMAX introduction course page (UPPMAX).
Monthly Workshop Series: Whisper Transcription demonstration, starting February 4
Collaboration between UPPMAX and CDHU
OpenAI’s Whisper model makes it possible run fast, accurate, and secure automatic transcriptions of audio locally through Uppmax. This is even possible for files that are several hours long and/or which contain sensitive or personal information. In this demonstration, an Uppmax applications expert working with Humanities and Social Sciences researchers and CDHU will provide information about getting started with Whisper on their systems.
When: choose among February 4, March 4, April 4, or May 5
Where: hybrid event (Uppsala and online)
For more information, please visit the event calendar of Digital Humanities and Social Science, Uppsala Univeristy.
ENCCS training
Online workshop: Julia for High-Performance Data Analysis (Online), 4 - 7 February
Abstract: This online workshop will start by briefly covering the basics of Julia’s syntax and features, and then introduce methods and libraries which are useful for analyzing and visualizing large datasets using dataframes and visualization packages.
Detailed information at webpage: the HPDA with Julia workshop page (ENCCS).
Time: Feb. 4-7, 09:00-12:00 (CET) (2025).